Despite the files (server.properties, for instance) being saved as UTF-8 files, and the JVM automatically picking up that FreeBSD's file encoding is UTF-8, when a minecraft server starts up and reads the UTF-8 config file, it saves it back to disk as plain ASCII, with the unicode character mangled.

For example:
motd=♥ A Minecraft Server

Turns into:
motd=\u00E2\u0099\u00A5 A Minecraft Server

This also leads to problems with modded minecraft's config files, but I believe fixing this underlying issue will also solve that.